Slashdot Mirror
X-Prize to Award $10M for Fast Sequencing
Shipud writes "The X-Prize foundation has announced the $10 million Archon X PRIZE for Genomics — for the first privately financed group to sequence 100 human genomes in 10 days. The motivation is to create an incentive for faster, cheaper genome seqeunceing, heralding the era of preventative personalized medicine. The winner will also receive an extra $1,000,000 for sequencing the genomes of 100 additional people; among them Larry King and Stephen Hawking. Apparently this is the largest medical prize in history."
X-prize for first post!
lemonade was a popular drink and it still is
This was already covered by /. http://slashdot.org/article.pl?sid=06/10/04/151323 6 9 days ago.
keeps us all certain that the "editors" don't actually read slashdot.
How we know is more important than what we know.
In China, they have the same competition. But then you win and they send the bill to your family.
Onda Technology Institute
http://slashdot.org/article.pl?sid=06/10/04/151323 6
I, for one, don't welcome our fabulous editing underlords.
biopowered.co.uk - catalytically cracking triglycerides for home automotive use since 2008. Just say no to big oil!
Gattaca
When his defense asked, "Which computer has Jon Johansen trespassed upon?" the answer was: "His own."
Stephen Hawking I can understand but why is Larry King included. What makes him worthy of having his genomes sequenced.
here : http://slashdot.org/article.pl?sid=06/10/04/151323 6
Ceci n'est pas une Signature !
Welcome to DNA RAR. We have developed an exclusive peptide encryption method using random RNA sequences as hash key while pinching out false exclusives, just for yucks.
DNA RAR allows all of your genetic material to be encoded within an encryption program that is both free source code and open source.
All of this fucking harcore science for DMCA.
Woo!
A million bucks is a million bucks. If they've already got it going, presumably it'd be worth it.
In short:
An intresting detail:
Note that Human Genome Project mapped and sequenced only some 3Gbp. And that was considered to be whole genome. Basically X-Price want winner to sequence all 46 cromosomes. This sounds quite difficult as the method have to be sure that is has sequenced both of the cromosomes (from a pair), not just the other one twice. And this must be valid all the 3Gbp. By bet? The working method just sequences emultiple chromosomes and determines the exact basepairs statically.
Should have been "Darwin Award", but that was taken already...
In modern America, researchers search for cures to genetic disease in Soviet Russia, the party cures your genetic defect called life...by sending you to the gulag for "research"
Learn to know, the dark side of the force, and you will achieve a power greater than any Jedi...the power to save your w
I've been browsing the site now for some time and haven't found a single shread of evidence for this "extra price". I call bullshit. It's just a joke to mock the slashdot "editors".
So we don't repeat him.
* Winners compare their achievements to their goals, losers compare theirs to that of others.
My cash is on CodonDevices. George Church has an incredible new sequencing technology, and he's making it open source. I know some of the peeps there writing software, and between the tech and the IT team, they'll be able to generate and handle the data - the big sequencing companies ought to be scared...
Genes are your Destiny.
Too bad the sequencing research these days is not so much focusing on fast sequencing (though that is of course still a major concern), as it is on accurate sequencing. One of the problems bio-folk are encountering is that the human genome is relatively easy to sequence: you can get all your DNA from one individual (so you only need to worry about getting two unique DNA sequences getting mixed up in the final result, one from the male and female parents) and there isn't as much repetition as compared to say, mosquito genomes. Further, when studying things like mosquitos, the shotgunning techniques currently need to use DNA from whole portions of a population, say 50 or more individuals (AFAIK), so your final result doesn't really represent any one member; a lot of useful information is lost this way.
Anyway, just my semi-educated two cents. I'm CS, so what do I know? Well, I'm told it's NP hard, so... good luck with getting that 10 Mil and still having an accurate result.
The snow doesn't give a soft white damn whom it touches. -- ee cummings
You mean government doesn't have to fund all research by forcibly taking money from its citizens?
Slashdot only has one day left to dupe this another 98 times if they hope to claim the prize...
TFA? Whats that?
any true revolutions at a company or other entity that allows this level of an improvement over current sequencing tech will have so much VC money (or parent company cash) rolling in that $10 million won't even be worth the time for application. Then when the tech is validated and ready for use, they wouldn't have time to cash the check for $10 million while the billions are rolling in.
For those of you in other fields, imagine in the next jet propulsion X prize was $10 million to the first group to come up with a working drive capable of 20% of the speed of light within a day of ignition. Or how about a single computer CPU capable of processing 100 peta flops. Or a system capable of cracking a gallon of water but using only 100 joules of electricity.
Sure, some day these may all be possible, but right now they are pie in the sky at best.
They'll try to make a super baby from the 100 people and it'll get the brains of Larry King and ALS from Hawking..
Reminds me of a George Bernard Shaw quote (mis-attributed sometimes to Einstein I think). When it was suggested to him by a beautiful woman that they could make super-babies together, he replied:
"But what if they had my looks and your brains?
This was already covered, but new news I found about the X Prize Cup got rejected yesterday. :(
Isn't a discussion about the new events at this year's exhibition worthwhile? Oh well.
http://www.xprizecup.com/
With regards to this post, and the following post about 98 % coverage.
The quality (i.e. the error rate) must be 0.01%, which is the convention adopted as the Bermuda Standard back when large scale sequencing was becoming mainstream, and the first genomes (of bacteria) were being produced. The coverage must be 98%. Usually, the last 2% are virtually impossible to elucidate because they are so repetitive (e.g. around centromeres) that you cannot tell how many copies of the repeats there are. The repeat regions are much larger than the contiguous sequences of about ~1000 bases you get from the sequencing machine "reads", so unambiguously assembling the overlapping reads becomes impossible. Luckily, the most useful data is in the 98% percent that is easier to sequence.
With regards to the 6GB, the human genome project has sequenced much, much more than 3GB. What you end up with is an assembly of the sequence into 3GB based on the consensus of the genomic DNA used (they did not do just one individual). The differences between the individuals are also recorded, largely as Single Nucleotide Polymorphisms (SNPs). These SNPs form the majority of the differences between the 2 copies of chromosomes (23*2) we all have.
On a technical note, all of the new techniques that are being commercialized for very high throughput sequencing (e.g. 454) rely VERY heavily on computer power to assemble the results into meaningful, long sequences. If you though assembling the Human Genome Project would be a lot of work with its 1000 base reads, try assembling data from the new techniques, with their 100 or 25 base reads (depending on the technology you use). The less overlap you have between reads, the harder it is to resolve the assembly unambiguously...
The real goal here is to be able to genetically analyze people, and not what the article claims, to help them. Like any tool, it can be used for good and for bad. Like any new technology, such as aviation, or nuclear, it will probably be first tested out by the military or at least tested out in all its negative connotations before it is put to work for public good. Such people-analyzing technology will allow a new form of racism, or at least some form of historical revenge-taking. How would you like to know that your genetic makeup is 26% of a genetic class #AA5FE most prevalent in lower Poland, Checz Republic, Northern Ireland and Southern Iran, then 32% is class #BY98Z most prevalent in southern Sweden, 5% class #CCXFE most prevalent in ancient Greece(from archeological bone-marrow extracts) but practically extinct (therefore you'll be heavily studied and bread with similar people containing this ancient Greek recessive gene to study the ancient Greeks better, especially by people who have an axe to grind with the ancient greeks), 2% class #FE3X2 of a gene most prevalent in North Korea and South America, etc. Imagine if you possessed a gene that's most prevalent in North Korea, Iran, Iraq, Libya (wait, Libya no longer belongs to this axis of evil group), imagine if such a gene was found that's most prevalent in the countries that happen to fall into the current axis-of-evil vogue category. Aha! We found the evil gene, now let's go find people that have it in the USA, and send them to camps like the japanese were in WW2. There'll be people looking for the callousness gene, the atheist gene, the deist gene, the child-molester gene, the communist-gene, the capitalist-gene, and try to put people to death based on it, in the name of the good of society, just like witches were burned alive at the stake for being found guilty of mingling with the devil. For fire has a purifying power, it cleanses your soul of your sins, and being burned alive is like passing through a purgatory on this earth, therefore your soul has a higher chance of entering Heaven instead of Hell in the afterworld, so people who execute you at the town square like this do it out of brotherly love, in the name of saving your soul from eternal damnation, while the crowd cheers on.
Sometimes I just don't wanna know "who" exactly I am, or where I come from, or where the other guy next to me comes from. It's enough of a divide that he looks different, such as he's black, but now we're gonna fine tune the difference seeking amongst people, and turn man against man not because one looks black the other white, or because even if they look the same, one is serbian the other croatian, now we'll be able to turn people against each other and have them exterminate each other even when they look the same, speak the same language, hold the same culture, but hey!, they are genetically different! So go fight, compete, push your "kind" higher, push other "kinds" lower, as opposed to the old your nation higher, other nations lower, now you'll be able to do it even within nations better! There are native americans on reservations studying in schools, and here and there there is a blonde kid amongst them, even though his parents are both indian-looking, but carry some blonde recessive gene from all the past intermarriages. This blonde kid may think himself as indian, even though he might have a hard time dealing with his looks standing out in a crowd. But even indian looking people are told today they are not indian. They are told, look, here's your bloodline, your great great great gramma married a black guy, so that made your bloodline 1/2 native american, then 3 generations later your great great granpa married an italian, so that made it 1/4, and so on, 1/8, 1/16, 1/32, 1/64, 1/128th. The treaties signed by Abe Licoln giving this land to native americans do not apply to you, because the government has a policy to stop considering you indian once your genetic makeup falls below 1/64th native american, and 63/64th other. So it doesn't matter that you love nativ
your name is very appropriate.
We've known of the existence of bloodgroups for years, but I'm fairly sure nobody's been discriminated against on the basis of being O- or A+.
In fact, nobody really cares.
except the japanese. seriously. (ketsu eki gata).
Can someone explain what genome sequencing actually does? Does it "simply" give you a complete description of the base pairs of someone's DNA? Yes. Actually, even less than that. "Shotgun" sequencing give you a collection of random seqeunces of base pairs, ~1,000 BP long. You need quite a few of those to reassmeble the human genome, computationally. Or is it a little more complicated than that, telling you where the individual genes begin and end? What information can you derive when you know the sequence of all the base pairs? To determine that, you need to perfomr a computational analysis on the assembled (see above) genome. Gene prediction algorithms are relatively relaible, although there is room for improvement and error reduction. You can derive a lot of information, depending on how sophisticated the algorithms that your use are, and how much of an error margin you allow yourself: the beginning and end of genes, region that control gene transcription (that's copying DNA to RNA) and gene translation (that's RNA to protein), alternative splicing (differnt transcripts of the same gene). Once you have your translated protein sequences, you can do a lot more with that: predict their 3D atomic structure, look for similar proteins in other organisms, discover rates of evolution, detect hidden viruses in the genome, locate disease causing mutations....